[2023-03-18 01:53:08,424] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:53:08,424] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:53:08,424] [INFO] DQC Reference Directory: /var/lib/cwl/stga1385f7b-0b7a-4549-8eb3-654e4458c1ce/dqc_reference
[2023-03-18 01:53:09,513] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:53:09,514] [INFO] Task started: Prodigal
[2023-03-18 01:53:09,514] [INFO] Running command: cat /var/lib/cwl/stgf5ef5dde-ee99-4cb4-a3dc-35179f48e4df/OceanDNA-b45584.fa | prodigal -d OceanDNA-b45584/cds.fna -a OceanDNA-b45584/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:53:24,716] [INFO] Task succeeded: Prodigal
[2023-03-18 01:53:24,716] [INFO] Task started: HMMsearch
[2023-03-18 01:53:24,716] [INFO] Running command: hmmsearch --tblout OceanDNA-b45584/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1385f7b-0b7a-4549-8eb3-654e4458c1ce/dqc_reference/reference_markers.hmm OceanDNA-b45584/protein.faa > /dev/null
[2023-03-18 01:53:24,876] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:53:24,877] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf5ef5dde-ee99-4cb4-a3dc-35179f48e4df/OceanDNA-b45584.fa]
[2023-03-18 01:53:24,891] [INFO] Query marker FASTA was written to OceanDNA-b45584/markers.fasta
[2023-03-18 01:53:24,893] [INFO] Task started: Blastn
[2023-03-18 01:53:24,893] [INFO] Running command: blastn -query OceanDNA-b45584/markers.fasta -db /var/lib/cwl/stga1385f7b-0b7a-4549-8eb3-654e4458c1ce/dqc_reference/reference_markers.fasta -out OceanDNA-b45584/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:53:25,439] [INFO] Task succeeded: Blastn
[2023-03-18 01:53:25,439] [INFO] Selected 5 target genomes.
[2023-03-18 01:53:25,440] [INFO] Target genome list was writen to OceanDNA-b45584/target_genomes.txt
[2023-03-18 01:53:25,443] [INFO] Task started: fastANI
[2023-03-18 01:53:25,443] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5ef5dde-ee99-4cb4-a3dc-35179f48e4df/OceanDNA-b45584.fa --refList OceanDNA-b45584/target_genomes.txt --output OceanDNA-b45584/fastani_result.tsv --threads 1
[2023-03-18 01:53:28,515] [INFO] Task succeeded: fastANI
[2023-03-18 01:53:28,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1385f7b-0b7a-4549-8eb3-654e4458c1ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:53:28,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1385f7b-0b7a-4549-8eb3-654e4458c1ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:53:28,515] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:53:28,515] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:53:28,516] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-18 01:53:28,516] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45584/tc_result.tsv
[2023-03-18 01:53:28,516] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:53:28,516] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:53:28,516] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1385f7b-0b7a-4549-8eb3-654e4458c1ce/dqc_reference/checkm_data
[2023-03-18 01:53:28,526] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:53:28,529] [INFO] Task started: CheckM
[2023-03-18 01:53:28,530] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45584/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45584/checkm_input OceanDNA-b45584/checkm_result
[2023-03-18 01:54:11,969] [INFO] Task succeeded: CheckM
[2023-03-18 01:54:11,969] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 7.34%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-18 01:54:11,972] [INFO] ===== Completeness check finished =====
[2023-03-18 01:54:11,972] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:54:11,973] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45584/markers.fasta)
[2023-03-18 01:54:11,973] [INFO] Task started: Blastn
[2023-03-18 01:54:11,973] [INFO] Running command: blastn -query OceanDNA-b45584/markers.fasta -db /var/lib/cwl/stga1385f7b-0b7a-4549-8eb3-654e4458c1ce/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45584/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:54:12,890] [INFO] Task succeeded: Blastn
[2023-03-18 01:54:12,891] [INFO] Selected 21 target genomes.
[2023-03-18 01:54:12,891] [INFO] Target genome list was writen to OceanDNA-b45584/target_genomes_gtdb.txt
[2023-03-18 01:54:12,911] [INFO] Task started: fastANI
[2023-03-18 01:54:12,911] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5ef5dde-ee99-4cb4-a3dc-35179f48e4df/OceanDNA-b45584.fa --refList OceanDNA-b45584/target_genomes_gtdb.txt --output OceanDNA-b45584/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:54:22,877] [INFO] Task succeeded: fastANI
[2023-03-18 01:54:22,880] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:54:22,880] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_018645725.1	s__MB11C04 sp018645725	84.1196	363	458	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722545.1	s__MB11C04 sp002722545	79.7349	216	458	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002500665.1	s__MB11C04 sp002500665	77.2166	95	458	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	98.37	95.55	0.93	0.84	7	-
--------------------------------------------------------------------------------
[2023-03-18 01:54:22,880] [INFO] GTDB search result was written to OceanDNA-b45584/result_gtdb.tsv
[2023-03-18 01:54:22,880] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:54:22,881] [INFO] DFAST_QC result json was written to OceanDNA-b45584/dqc_result.json
[2023-03-18 01:54:22,881] [INFO] DFAST_QC completed!
[2023-03-18 01:54:22,881] [INFO] Total running time: 0h1m14s